.TH MSI2LMP "1" "v3.9.11" "2024-09-06"
.SH NAME
.B MSI2LMP
\- Converter for Materials Studio files to LAMMPS

.SH SYNOPSIS
.B msi2lmp
[-help] <ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]

.SH DESCRIPTION
.PP
.B MSI2LMP
is a tool bundled with LAMMPS to aide in the conversion of simulation
inputs from Biovia's Materials Studio software for use with LAMMPS.
It is a standalone program that generates a LAMMPS data file based on
the information in an MS .car file (atom coordinates), an .mdf file
(molecular topology and atom types) and an .frc (forcefield parameters)
file.  The .car and .mdf files are specific to a molecular system while
the .frc file is specific to a forcefield (variant).  The only coherency
needed between .frc and .car/.mdf files are the atom types.
.PP

.SH OPTIONS
.TP
\fB\-h\fR, \fB\-help\fR,
Print detailed help message to the screen and stop.
.TP
\fB\<ROOTNAME>\fR
This has to be the first argument and is a
.B mandatory
argument. It defines the root of the file names; i.e. for a
.B <ROOTNAME>
of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
in the current working directory.
.B msi2lmp
will then read and process those files according to its remaining settings.
All other settings are optional and have defaults as listed.
.TP
\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
The \-c or \-class option selects the force field class, i.e which pair
styles and bond styles and so on are required in the LAMMPS input file.
Class I or class 1 uses similar combination of functional forms as Amber
and Charmm force field and support the force fields 
.B cvff
and
.B clayff.
Class II or class 2 corresponds to the more complex force fields
.B COMPASS
and
.B pcff.
Class O or class 0 finally is an experimental and incomplete extension
and supports generating output for
.B OPLS-AA
.TP
\fB\-f <ffname>\fR, \fB\-frc <ffname>\fR
The \-c or \-frc option allows the selection of the force field parameter
file
.B<ffname>.frc.
Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug,
pcff, compass_published, cff91, and oplsaa. If the argument is a pathname,
i.e. it starts with a '.' or a '/', then this absolute path is used to read
the force field, otherwise
.B msi2lmp
will look in the folder pointed to by the environment variable
$MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current
directory. The extension '.frc' is appended, if missing.
Default is to look for the cvff.frc force field file.
.TP
\fB\-p <loglevel>\fR, \fB\-print <loglevel>\fR,
Selects the amount of information messages about the progress of the
conversion printed to the screen.
.B <loglevel>
can be a number from 0 (silent except for errors) to 3 (very detailed).
.TP
\fB\-i\fR, \fB\-ignore\fR,
Ignore errors about missing parameters and use 0.0 for the respective
force constants making these no-ops. Is correct to be used for a few
molecules and settings, but often an indication, that either the atom
type assignment have errors, or the force field file is missing entries.
.TP
\fB\-n\fR, \fB\-nocenter\fR,
Do not center the box around the (geometrical) center of the atoms,
but around the origin. Default is to recenter.
.TP
\fB\-o\fR, \fB\-oldstyle\fR,
Write out a data file without style hint comments to be compatible
with old LAMMPS versions. Default is to write out those comments.
.TP
\fB-s <x> <y> <z>\fR, \fB-shift <x> <y> <z>\fR,
Shift the entire system (box and coordinates) by a vector
(default: 0.0 0.0 0.0).
.TP

.SH EXAMPLES

msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc

msi2lmp benzene-class1 -c I

msi2lmp decane -c 0 -f oplsaa


.SH COPYRIGHT
© 2003--2024 Sandia Corporation

This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 2 as
published by the Free Software Foundation.

This package is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

